BN1266 Genetic Spatial Mapping Report

Genetic Spatial Mapping Plot

This plot shows the spatial genetic mapping results across different tissues.

Cauchy Combination Result

This table presents the results of the Cauchy combination test, summarizing the genetic associations.

Annotation P Cauchy P Median
Layer 4 1.8417e-04 2.3074e-03
Layer 5 4.3559e-04 2.1270e-03
Layer 3 4.4054e-04 4.3752e-02
Layer 6 8.7640e-04 2.5720e-03
Layer 2 7.6591e-03 1.0010e-01
Layer 1 6.7059e-01 5.5361e-01
WM 8.9677e-01 4.4695e-01

Diagnosis Manhattan Plot

The Manhattan plot shows the association of SNPs with the top associated gene across the genome.

Gene Expression and GSS Distribution

Select a gene to view its expression distribution and gene specificity score (GSS).

Expression Distribution
SNCA Expression Distribution
Gene Specificity Score (GSS)
SNCA GSS Distribution

Top 50 Gene Diagnostic Info

This table lists the top 50 genes based on diagnostic criteria, including the gene specificity score (GSS) and PCC.

Gene Annotation Median GSS PCC
SNCA Layer 5 2.7539 0.7058
TUBB2A Layer 5 3.0000 0.6914
TUBB3 Layer 5 2.6748 0.6905
SH3GL2 Layer 5 2.5840 0.6865
STMN1 Layer 5 2.5508 0.6793
MORF4L1 Layer 4 2.3965 0.6769
EEF1A2 Layer 5 2.5391 0.6750
STMN2 Layer 5 3.1191 0.6745
SYN2 Layer 5 3.0605 0.6697
QDPR Layer 6 2.5869 0.6671
PINK1 Layer 4 2.3213 0.6666
SLC24A2 Layer 5 2.6016 0.6641
TUBB Layer 5 2.4316 0.6633
SPOCK1 Layer 6 2.7217 0.6623
ENO2 Layer 5 2.7129 0.6620
CEND1 Layer 6 2.3262 0.6606
SYP Layer 5 2.4102 0.6606
ANXA6 Layer 6 2.4668 0.6603
PRKAR1B Layer 5 2.6221 0.6602
RTN1 Layer 5 2.6133 0.6577
MTCH1 Layer 6 2.5508 0.6560
ATP1A3 Layer 6 2.4512 0.6559
SEZ6L2 Layer 5 2.3965 0.6553
APBB1 Layer 4 2.3467 0.6550
ARL6IP1 Layer 5 2.5635 0.6548
FKBP8 Layer 6 2.4844 0.6482
DNM1 Layer 5 2.4082 0.6476
ATP5F1B Layer 5 2.2266 0.6473
ELAVL2 Layer 5 2.3809 0.6465
AP2M1 Layer 6 2.5840 0.6449
MAPK8IP2 Layer 5 2.2773 0.6447
IQSEC1 Layer 4 2.3125 0.6441
PJA2 Layer 5 2.3340 0.6437
TUBA4A Layer 5 2.3027 0.6431
NAPB Layer 5 2.4453 0.6425
KIF3C Layer 5 2.2969 0.6418
FXYD6 Layer 5 2.6191 0.6397
DCLK1 Layer 5 2.4121 0.6390
VAMP2 Layer 6 2.4238 0.6382
YWHAG Layer 5 2.6660 0.6375
GAP43 Layer 5 2.4785 0.6358
RTL8C Layer 6 2.5723 0.6337
PREPL Layer 5 2.4395 0.6331
NEFL Layer 5 2.3711 0.6326
CABP1 Layer 6 2.4209 0.6312
CALY Layer 4 2.1816 0.6310
CAPNS1 Layer 5 2.3682 0.6282
MAP1LC3A Layer 5 2.3125 0.6281
APP Layer 5 2.3340 0.6280
NCALD Layer 5 2.2168 0.6274

Running Info

Click to view detailed run information and parameters.

gsMap Version: 1.73.0

Parameters:

  • Sample Name: BN1266
  • Trait Name: PD
  • Summary Statistics File: /mnt/data/projects/ASAP/ST/gsMAP/GWAS_nallsEtAl2019_allSamples_allVariants.sumstats.gz
  • HDF5 Path: /mnt/data/projects/ASAP/ST/gsMAP/st_anndata_h5ads/st_adata_BN1266_for_gsmap.h5ad
  • Annotation: smoothed_label_s5
  • Spatial LDSC Save Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1266/spatial_ldsc
  • Cauchy Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1266/cauchy_combination
  • Report Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1266/report/PD
  • gsMap Report File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1266/report/PD/BN1266_PD_gsMap_Report.html
  • Gene Diagnostic Info File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1266/report/PD/BN1266_PD_Gene_Diagnostic_Info.csv
  • Report Generation Date: 2025-04-11 03:01:36
  • Number of Processes: 10
  • Spending Time: 0h 2m